Fix bug that prevented infile being specificed with "-I"
Fix bug that prevented infile being specificed with "-I"

AntonioJBT/CGATPipeline_core,CGATOxford/CGATPipelines,CGATOxford/CGATPipelines,AntonioJBT/CGATPipeline_core,CGATOxford/CGATPipelines,AntonioJBT/CGATPipeline_core,CGATOxford/CGATPipelines,CGATOxford/CGATPipelines,AntonioJBT/CGATPipeline_core